Exploring endometrial cellular heterogeneity and its role in endometriosis using single-cell transcriptomics

Thesis

The human endometrium, the inner mucosal lining of the uterus, undergoes cycles of shedding, regeneration, growth, and differentiation on a monthly basis in response to steroid hormones. In endometriosis, endometrial-like cells grow outside of the uterus, and are associated with debilitating chronic pain and subfertility that can have a substantial negative impact on quality of life. Yet, it is not fully understood how the endometrium achieves its immense regenerative capacity and whether the cellular make-up of the endometrium in health and endometriosis differs. Studies profiling the endometrium at the single-cell level have so far analysed only a limited number of cells and samples, making it difficult to disentangle the inherent heterogeneity of this dynamic tissue. In this thesis I aimed to generate a comprehensive cellular map of the endometrium in a large set of donors with/without endometriosis both during natural menstrual cycles and when taking exogenous hormonal therapy. I hypothesised that by analysing a large set of endometrial biopsies we can uncover novel cell populations and disease-specific transcriptomic signatures.

The single-cell map presented in this thesis consists of ~600,000 whole cells and nuclei from 90 individuals, and was compiled by integrating data newly generated during my studies with two previously published datasets. Focusing on the epithelial and mesenchymal cell lineages, I defined novel cell populations that appear around the time of ovulation and window of implantation. Moreover, I observed cell populations specific to taking various forms of exogenous hormonal therapy. Additionally, I utilised the in vivo endometrial cellular map to dissect the cellular heterogeneity of in vitro endometrial organoids and organoid-stromal cell cocultures. Analysing ~100,000 cells, I described a population of cells expressing MUC5B, PAEP, and TFF3 as a feature present in organoids from donors with endometriosis. Altogether, the cellular maps of the endometrium in vivo and in vitro presented in this thesis have the potential to serve as a great resource to further study endometrial function and associated pathologies, as well as guide the development of novel clinical in vitro models of the endometrium.

Authors: Marečková, M

• DOI: 10.5287/ora-00ne0jevm
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: single-cell genomics; endometrium; organoids; endometriosis
• Subjects: Human cell culture; Endometriosis; Messenger RNA; Endometrium; Cell coculture; Genomics